The cell based in Sharqiya province was implicated in attacks on "security posts and military apparatus in North Sinai, which killed many members of the armed forces and police force," the ministry said in a statement.
Members were also accused of plotting other attacks on vital infrastructure in the region, it added.
Police found automatic rifles and ammunition during the raid on a site that had been used as a weapons and explosives training centre.
Security forces in Cairo also detained nine people and seized weapons and explosive devices, the ministry said.
Egyptian security forces have been increasingly targeted by extremists since the army overthrew Islamist president Mohamed Morsi in 2013.
An insurgency by an Islamic State group affiliate based in North Sinai has killed hundreds of police and soldiers, as well as civilians.